algbio/MFD-ILP

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MIT License
Created about 3 years ago
Updated over 1 year ago

algbio/MFD-ILP

algbio

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Fast and exact ILP-based solvers for the Minimum Flow Decomposition problem, and variants of it.

themisto

Space-efficient pseudoalignment with a colored de Bruijn graph

GraphChainer

An accurate aligner of long reads to a variation graph, based on co-linear chaining

SBWT

Code for the paper Succinct k-mer Set Representations Using Subset Rank Queries on the Spectral Burrows-Wheeler Transform (SBWT)

matchtigs

Minimum plain text representation of kmer sets

emerald

EMERALD calculates safety-windows by exploring the suboptimal alignment space

metaflow

MetaFlow is a program for community profiling of a metagenomic sample

VOMM

Space-efficient variable-order Markov models

PerformanceMPC

Efficient C++ implementations of different fast algorithms for Minimum Path Cover

mfd-safety

emerald-analysis

Jupyter Notebook

Introduction-to-Applied-Bioinformatics

Genome assembly - From theory to practice (and back)

practical-omnitigs

A repository to conduct experiments with omnitig-related models for genome assembly.

Jupyter Notebook

optimized-fd

RobustFlowDecomposition

Flow Decomposition Under Uncertainty

SRFAligner

spl-IsoQuant

A pipeline for processing Spl-Iso-Seq data

anchors-in-chaining

panvc-founders

Instructions and examples for using PanVC with founder sequences

bwtCluster

Space-efficient clustering for metagenomic reads

alignment-safety

Jupyter Notebook

founderblockgraphs

Constructs segment repeat-free founder block graphs from multiple sequence alignments

efg-mems

MEM finding on (elastic founder) graphs

panvc3-experiments

Experiments for evaluating PanVC 3